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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><!--Converted with LaTeX2HTML 98.1p1 release (March 2nd, 1998)originally by Nikos Drakos (nikos@cbl.leeds.ac.uk), CBLU, University of Leeds* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan* with significant contributions from: Jens Lippmann, Marek Rouchal, Martin Wilck and others --><HTML><HEAD><TITLE>EXAMPLE 2</TITLE><META NAME="description" CONTENT="EXAMPLE 2"><META NAME="keywords" CONTENT="FEBS98-html"><META NAME="resource-type" CONTENT="document"><META NAME="distribution" CONTENT="global"><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"><LINK REL="STYLESHEET" HREF="FEBS98-html.css"><LINK REL="next" HREF="node16.html"><LINK REL="previous" HREF="node14.html"><LINK REL="up" HREF="node13.html"><LINK REL="next" HREF="node16.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html229" HREF="node16.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html226" HREF="node13.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html220" HREF="node14.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html228" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A> <BR><B> Next:</B> <A NAME="tex2html230" HREF="node16.html">EXAMPLE 3</A><B> Up:</B> <A NAME="tex2html227" HREF="node13.html">Sample foldings</A><B> Previous:</B> <A NAME="tex2html221" HREF="node14.html">EXAMPLE 1</A><BR><BR><!--End of Navigation Panel--><H2><A NAME="SECTION00082000000000000000"> E<SMALL>XAMPLE 2</SMALL></A></H2><P>Important alternative foldings might not appear in the <I>energy dot plot</I> if <!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">is too small. This is especially true in the folding of shortsequences. When the short sequence: <BR> <TT>AAGGGGUUGG UCGCCUCGACUAAGCGGCUU GGAAUUCC</TT>, <BR>is folded, also with default parameters, asingle optimal folding is computed. However, the <I>energy dot plot</I> contains onlythe optimal, black dots from Figure <A HREF="node15.html#EX2P">15</A>. Changing the windowsize would not reveal anything new. When the value of P is increasedto 25 (25%), the <I>energy dot plot</I> now reveals a very distinct alternate foldingas shown in Figure <A HREF="node15.html#EX2P">15</A>. The <I>mfold</I> program now computes 2foldings, plotted in Figure <A HREF="node15.html#EX2S">16</A>, using the default value of W.<P><BR><DIV ALIGN="CENTER"><A NAME="EX2P"> </A><A NAME="844"> </A><TABLE WIDTH="50%"><CAPTION><STRONG>Figure 15:</STRONG>The <I> energy dot plot</I> for ``Example 2'' sequence with <!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">increased to 25%of 10.1, or 2.5 kcal/mole. The value of <!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">in the plot may be lessthan this maximum value, since there may be no base pairs in foldingsthat are <I> exactly</I> <!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">from the minimum free energy. The 2green dots represent base pairs that can be in foldings with <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">between -9.4 and -8.6 kcal/mole. These numbers are -8.6 and -7.9 forthe yellow dots. In this case, the black dots comprise the optimalfolding, and the yellow dots comprise the single suboptimal foldingthat is computed. The green dots would only be found in a folding ifthe value of W were lowered sufficiently.</CAPTION><TR><TD><IMG WIDTH="358" HEIGHT="353" SRC="img124.gif" ALT="\begin{figure}\centering\epsfig{file=1b-again_zoom.ps}\end{figure}"></TD></TR></TABLE></DIV><BR><P><BR><DIV ALIGN="CENTER"><A NAME="EX2S"> </A><A NAME="847"> </A><TABLE WIDTH="50%"><CAPTION><STRONG>Figure 16:</STRONG>The 2 predicted foldings for the ``Example 2''sequence. (a) The optimal folding with <!-- MATH: $\Delta G= -10.1$ --><IMG WIDTH="91" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img10.gif" ALT="$\Delta G= -10.1$">kcal/mole. (b) The suboptimal fold (<!-- MATH: $\Delta G= -7.9$ --><IMG WIDTH="83" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img11.gif" ALT="$\Delta G= -7.9$">kcal/mole)found after refolding with `P'=25.</CAPTION><TR><TD><IMG WIDTH="298" HEIGHT="371" SRC="img125.gif" ALT="\begin{figure}\centering\subfigure[]{\epsfig{file=1b-again_1_zoom.ps,width=0.3\......subfigure[]{\epsfig{file=1b-again_2_zoom.ps,width=0.3\textwidth} }\end{figure}"></TD></TR></TABLE></DIV><BR><P><HR><!--Navigation Panel--><A NAME="tex2html229" HREF="node16.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html226" HREF="node13.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html220" HREF="node14.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html228" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A> <BR><B> Next:</B> <A NAME="tex2html230" HREF="node16.html">EXAMPLE 3</A><B> Up:</B> <A NAME="tex2html227" HREF="node13.html">Sample foldings</A><B> Previous:</B> <A NAME="tex2html221" HREF="node14.html">EXAMPLE 1</A><!--End of Navigation Panel--><ADDRESS><TABLE><TR><TD><IMG SRC=img/shield16.gif HSPACE=20></TD><TD><I>Michael Zuker <BR>Institute for Biomedical Computing<BR>Washington University in St. Louis<BR>1998-12-05</I></TD></TR></TABLE></ADDRESS></BODY></HTML>⌨️ 快捷键说明
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